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Vaati was born a Minish, a tiny race equal in size to a human thumb. When Vaati was a small boy, he was taken in by the Minish sage Ezlo to be his apprentice. While Vaati learned several valuable things under his teaching, he became fascinated when he learned of the evil that could come from the heart. Vaati became twisted and corrupted by this and began to seek out this evil for himself.

The turning point came when Vaati's master fashioned a powerful cap that could grant wishes as a gift for the humans. Vaati unexpectedly stole the cap when his master entered the room. Vaati then used the cap to grant his wish, to become the most powerful sorcerer in the world. Vaati transformed into a Hylian mage and explained to Ezlo his plan to obtain the mystical Light Force at the upcoming Picori Festival to obtain god-like power. Vaati then cursed his master using his newfound magic, transforming him into a green hat shaped like a bird so that he could not stop him.

At the Picori Festival, Vaati took part in the centennial duel tournament and won it, allowing him to touch the sacred blade of the Minish, that seals the chest holding what he thought to be the Light Force. When the chest was brought before him, he used his magic to break the seal on the chest, releasing the evil forces inside. However, he was distraught not to see the Light Force he was seeking. He turned the young Princess Zelda to stone and continued his search for the Light Force.

The young boy Link is asked to stop Vaati and break the curse on Zelda. He must find the Four Elements and infuse them with the broken blade. He ventures on his quest, and successfully gathers the Elements. However, during his quest, the good King of Hyrule is possessed by Vaati, who uses the soldiers of Hyrule to help his search for the Light Force. Link sneaks into Hyrule castle and refuses his blade with the elements, turning his White Sword into the Four Sword. However, when he has the power to stop Vaati, he discovers that Hyrule Castle has been turned into a dark, dank shadow of its former self. However, he braves the many obstacles there and encounters Vaati. Vaati turns himself into three forms before admitting defeat. Link breaks the curse on Zelda, and Vaati is sealed within the Four Sword.

Appearing from nowhere, Vaati, now a Wind Mage (unlike in The Minish Cap) and solely taking the form of a flying eyeball-type monster, took to kidnapping any maidens he fancied. A number of heroes fought against him, but they all failed to defeat him. One day a mysterious boy carrying a "cursed" blade used the powers of the sword to split into four beings, and used this advantage to weaken Vaati and seal him inside the blade that the people would eventually name the "Four Sword".

There is some controversy among theorists as to whether this back story is covered in the end of The Minish Cap and exaggerated over time like the Imprisoning War, or a completely different event yet to be covered.

One day Zelda senses that the seal holding Vaati in the Four Sword weakening, and invites Link to help her investigate. Just before she checks the seal, Vaati escapes and captures her. He tells her that he shall reign again and that he will make Zelda his bride. Link is knocked out as he escapes to the Palace of Winds. Link, however, uses the Four Sword and travels to Vaati's palace. After adventuring through with his three copies, he discovers Vaati. The two engage in battle and Link defeats him, sealing Vaati up in the sword once again.

After Link rescued Zelda and sealed Vaati within the Four Sword, Hyrule was at peace, until Ganondorf stole the Dark Mirror and created Dark Link to kidnap Zelda and the Shrine Maidens and trick Link into drawing the Four Sword and releasing Vaati. During Link's adventure to save Hyrule, he found out that Vaati was not the real enemy, and that Ganondorf created Shadow Link to trick Link into releasing Vaati to distract him so Ganondorf could steal the Trident to transform into Ganon and take over Hyrule. Vaati's fate is unknown at the end of Four Swords Adventures, however. He seems to have died, but his death animation was more similar to being warped into the Dark World than the explosion deaths that are used most often to indicate an enemy has died.

In the manga adaption, he has a similar role, though it's unknown if he directly worked for Ganondorf was just being manipulated by him. Unlike the video game, it's actually Dark Link (who turned out to not be as evil as earlier depicted) who kills him, by destroying the Dark Mirror, which kept Vaati from being killed by the four Links.

Unlike other villains in the Zelda series who want to rule over Hyrule or obtain the Triforce, Vaati is a selfish self-serving villain who only seeks to obtain whatever he personally desires. Having been corrupted in learning the evil within the hearts of men he instinctively seeks to obtain his needs however possible, whether it be absolute power, or any maiden that catches his fancy. He is also very overconfident at times, laughing at and mocking anyone who challenges him. This often leads to him being shocked at his defeat at the hands of Link, asking how "someone with the power of the gods could be defeated by a child".

In Ocarina of Time, a possible cameo of Vaati can be seen. As an adult, if Link enters the Shooting Gallery in Kakariko Village, looking to the left will show three posters on the wall. These three posters contain an image of a creature strongly resembling Vaati in his wind mage form. However, this might have been a reference to other enemies, like Queen Gohma, who are characterized by their single eye. Furthermore, Ocarina of Time was released roughly five years prior to Vaati's first appearance in Four Swords. Also, another possible cameo can be seen in the Spirit Temple, above a Hylian inscription on the Eastern wall in the room containing the Anubis enemies.